Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000711
UniProt IDP49711
Primary gene name(s)CTCF
Synonym gene name(s)unknown
Protein nameTranscriptional repressor CTCF
Protein functionChromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region, ICR mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays a important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X- inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19. Plays a role in the recruitment of CENPE to the pericentromeric/centromeric regions of the chromosome during mitosis, PubMed:26321640. {ECO:0000269|PubMed:11743158, ECO:0000269|PubMed:16815976, ECO:0000269|PubMed:17827499, ECO:0000269|PubMed:18347100, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18550811, ECO:0000269|PubMed:18654629, ECO:0000269|PubMed:19322193, ECO:0000269|PubMed:26321640, ECO:0000269|PubMed:8649389, ECO:0000269|PubMed:9591631}.
Subcellular locationNucleus, nucleoplasm {ECO:0000250|UniProtKB:Q61164}. Chromosome {ECO:0000269|PubMed:26321640}. Chromosome, centromere {ECO:0000269|PubMed:26321640}. Note=May translocate to the nucleolus upon cell differentiation. Associates with both centromeres and chromosomal arms during metaphase. Associates with the H19 ICR in mitotic chromosomes. May be preferentially excluded from heterochromatin during interphase.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P49711
Gene Ontology
(Biological Process)
Complete annatation
chromosome segregation [GO:0007059];
covalent chromatin modification [GO:0016569];
DNA methylation [GO:0006306];
maintenance of DNA methylation [GO:0010216];
negative regulation of transcription, DNA-templated [GO:0045892];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
nucleosome positioning [GO:0016584];
positive regulation of gene expression [GO:0010628];
positive regulation of transcription, DNA-templated [GO:0045893];
protein localization to chromosome, centromeric region [GO:0071459];
regulation of centromeric sister chromatid cohesion [GO:0070602];
regulation of gene expression, epigenetic [GO:0040029];
regulation of gene expression by genetic imprinting [GO:0006349];
regulation of histone acetylation [GO:0035065];
regulation of histone methylation [GO:0031060];
regulation of molecular function, epigenetic [GO:0040030]
Gene Ontology
(Molecular Function)
Complete annatation
chromatin insulator sequence binding [GO:0043035];
RNA polymerase II core promoter proximal region sequence-specific DNA binding [GO:0000978];
sequence-specific DNA binding [GO:0043565];
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding [GO:0001228];
transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding [GO:0001078];
transcription corepressor activity [GO:0003714];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription regulatory region DNA binding [GO:0044212];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
chromosome, centromeric region [GO:0000775];
condensed chromosome [GO:0000793];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction115906
Phylogenetic treeP49711
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-0.03895500740575770.90529167876280.938931749402211
AZA vs. DISU0.04424388529758860.8611728793884860.991133096247651
AZA vs. IL7-0.03824047794023560.8424195772679820.999311006273513
AZA vs. SAHA-0.7190548253638450.003773215798490770.0513798147664407
DISU vs. CD30.07098702499570840.8445273114227260.894743090552866
DISU vs. IL7-0.09180625719245510.7153760902703660.927362160187958
DISU vs. SAHA-0.7619683677747410.00977335993325090.102004368112205
DMSO vs. AZA-0.02371259913893170.887505927890951
DMSO vs. CD30.004337999166450910.9891695984394690.992595750382375
DMSO vs. DISU-0.06969715148879950.7750932224732150.971526179368758
DMSO vs. IL7-0.007339777817830290.9674489283151970.993445226261602
DMSO vs. SAHA-0.7019302555422460.004459052082850470.0513373990171172
HIV vs. Mock in Activation0.1353636149811540.8276817139191380.999983755607037
HIV vs. Mock in Latency0.02065495993734270.9004217590099280.999834320637052
IL7 vs. CD30.007838093489526010.9805138380573140.988184346151237
SAHA vs. CD3-0.7045982442928730.0483867424468370.0963260513439675
SAHA vs. IL7-0.684043423399680.005533903214413720.0413914424632604
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change -1.283816652
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) FALSE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.165503 0.47281
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
0.96 0.782 0.68 0.666 0.82
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1X6H NMR - A=515-587.
2CT1 NMR - A=399-462.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
retropepsin cleaves 22944692

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found